There are 18 different skills in the game. They are ranked from 0% to 200%. The starting values for those skills at Level 1 are determined by the player's 7 basic attributes, but most of those skills would fall between 0% and 50%. Every time the player gains a level, he will be awarded skill points to be used to improve his skills, equal to 5 points + twice his Intelligence. The player may choose to "tag" 3 of the 18 skills. A tagged skill will improve at twice the normal rate.

How high a skill can be developed is affected by the character's Attributes - a character with a low Intelligence will not be able to boost their Science rating as high as a character with high Intelligence, for example. As skills grow higher in rating, they begin to cost more skill points to increase.

Books found throughout the game world can improve some of those skills permanently, although books are scarce early in the game. However, after a skill reaches a certain level, books no longer have any impact. Some NPCs can also improve skills via training.

Some skills can be improved while having certain items equipped. For example, equipping a lockpick would improve lock picking skills. Chems can also temporarily boost player's skills; however, they often have adverse effects such as addiction and withdrawal.

At character creation, the player may choose 2 optional traits for his or her character. Traits are special character backgrounds. Most traits have profound effects on gameplay. A trait normally contains one beneficial effect and one detrimental effect. They are listed under perks in the character sheet. Once a trait is chosen, it is impossible to change, except by using the "Mutate!" Perk that lets them change 1 Trait, 1 time.

Perks in the game are special elements of the level up system. Every 3 levels (or every 4 if the player chose the "Skilled" trait), the player is granted a perk of his or her choosing. Perks grant special effects, most of which are not obtainable via normal level up in the game, such as letting the player have more actions per turn. Unlike traits, most perks are purely beneficial - they are usually offset only by the infrequency of acquiring them.